[gmx-users] How to run MD simulation remotely

[charles k.davis]

Dear all,

My name is Charles, PhD student at National Institute of Technology,
Calicut, India.

I'm facing problem in giving Gromacs MD simulation job remotely (via ssh
command) in a Hybrid Cluster system. The system administrator told me to
copy paste the following script

*#! /bin/bash *
*#PBS - q small *
*#PBS -e errorfile.err *
*#PBS -o logfile.log *
*#PBS -l select=2:ncpus=16  *
*tpdir=`echo $PBS_JOBID | cut -f 1 -d .` *
*tempdir=/scratch/job$tpdir *
*mkdir -p $tempdir *
*cd $tempdir *
*cp -R $PBS_O_WORKDIR/* . *
*mpirun -np 32 -hostfile $PBS_NODEFILE mdrun_mpi -v -s input.tpr -c
output.gro*
*mv ../job$tpdir $PBS_O_WORKDIR/.*


in a text document and save it as* script.sh* and to submit the job run the
following command in terminal,



*qsub script.sh*
This method is not working for us. It will show that the job has been taken
up but soon it will vanish.

In our lab workstation (which we control directly, not remotely) we use the
following commands lines,


































*pdb2gmx -f Protein.pdb -o Protein.gro -p Protein.top -water spc
-ignhgenrestr -f UNK.gro -o posre_UNK.itp -fc 1000 1000 1000grompp -v -f
minim.mdp -c Protein.gro -p Protein.top -o Protein-EM-vacuum.tprmdrun -v
-deffnm Protein-EM-vacuum -c Protein_minimized.gro -nt 1editconf -f
Protein_minimized.gro -o Protein_minimized_box.gro -d 1.1 -bt cubicgenbox
-cp Protein_minimized_box.gro -cs spc216.gro -p Protein.top -o
Protein-water.grogrompp -v -f minim_water.mdp -c Protein-water.gro -p
Protein.top -o Protein-water.tprgenion -s Protein-water.tpr -o
Protein-water-ions.gro -p Protein.top -conc 0.15 -neutral -pname NA -nname
CLgrompp -v -f minim_water.mdp -c Protein-water-ions.gro -p Protein.top -o
Protein-EM-solvated.tprmdrun -v -deffnm Protein-EM-solvated -o
Protein_minim_traj_water.trr -c Protein_minimized_water.gro -e
minim_ener_water.edrmake_ndx -f Protein_minimized_water.gro -o
index.ndxgrompp -v -f nvt.mdp -c Protein_minimized_water.gro -p Protein.top
-o nvt.tprmdrun -v -deffnm nvtgrompp -f npt.mdp -c nvt.gro -t nvt.cpt -p
Protein.top -o npt.tpr -n index.ndx mdrun -v -deffnm nptgrompp -f md.mdp -c
npt.gro -t npt.cpt -p Protein.top -o Protein_md_1.tpr -n index.ndx mdrun -v
-deffnm Protein_md_1*

to do the simulation and keeping the files md.mdp, minim.mdp,
minim_water.mdp, npt.mdp and nvt.mdp in the work directory. We also keep
protein file as Protein.pdb and ligand file as UNK.pdb, UNK.gro and UNK.itp.

Can someone help me sort out this problem.

Many thanks,

Regards,

Charles K Davis
PhD Student
School of Biotechnology,
National Institute of Technology,
Calicut, Kerala, India-673 601
Cell Phone: +91 9495595458